Research Projects
Metabolic interactions in spatially structured microbial communities
- Role of metabolic interactions in shaping the spatial distribution and growth dynamics of biopolymer (e.g., alginate and chitin) degrading populations in microbial communities (Glen, Michael, Astrid, external pageJulia Schwartzman, Johannes Keegstra (Roman Stocker group))
- Metabolic interactions with non-growing bacteria (Gatwa, Kim)
- Evolution of cell-cell interactions in spatially structured bacterial communities (Divvya and Emanuele)
- Effect of contact-dependent antagonism on nutrient flow in bacterial communities (Astrid and Glen)
- Effect of bacterial motility on the efficiency of metabolic interactions (Roy)
- Role of bacterial stalks in metabolic interactions (Roy)
- Antibiotic tolerance in microbial cross-feeding communities (Guga)
- Pattern formation in multi-component biofilms (Guga, and external pageDave Johnson group)
- Evolution of microbial growth in nutrient limitation and co-limitation (Noelle, external pageMichael Manhart)
Group behavior and collective nutrient breakdown in microbial groups
- Impact of nutrient complexity on transitions between group and solitary behaviors in clonal groups (Glen, Johannes Keegstra (Roman Stocker group))
- Links between physiology, enzymatic capabilities and the strength of group behaviors (Glen and Ali Ebrahimi (external pageOtto Cordero group))
- Molecular and regulatory underpinnings of bacterial behavior during stages of biopolymer degradation (Glen, Astrid, Michael, external pageJulia Schwartzman, Johannes Keegstra (Roman Stocker group))
- How proteome efficient metabolism of individuals underlies metabolic interactions and the collective metabolism of microbial communities (Matthias)
Evolution of microbial interactions
- Experimental evolution of aggregation increases intracellular synergy in microbial populations (Glen and Astrid)
- The evolution of cell-cell interactions in spatially structured synthetic microbial communities (Divvya and Emanuele)
- How proteome efficient metabolism of individuals underlies metabolic interactions and the collective metabolism of microbial communities (Matthias)
- Factors that determine the degree of metabolic distribution in microbial ecosystems (Alyssa)
- Evolution of microbial growth in nutrient limitation and co-limitation (Noelle, external pageMichael Manhart)
Quantitative infection biology and antibiotic tolerance
- Phenotypic heterogeneity in salmonella populations (Alyson and Divvya)
- Activities of salmonella sub-populations using single cell transcriptomes (Alyson and Astrid)
- Antibiotic tolerance in microbial cross-feeding communities (Guga)
Nutrient limitation and co-limitation
- Phenomenological descriptions and models of microbial growth in nutrient co-limitation (Noelle, external pageMichael Manhart, Justus)
- Quantitative competition dynamics and resource interaction in microbial communities (Justus, external pageMichael Manhart, Noelle)
- Evolution of microbial growth in nutrient limitation and co-limitation (Noelle, external pageMichael Manhart)
- Changes in nutrient-use efficiency as a function of a second limiting nutrient (Noelle, external pageMichael Manhart)
- Molecular underpinnings of nutrient limited microbial growth (Noelle, Juanita Lara Gutierrez (Roman Stocker group))
Principles of metabolic pathway distribution
- How proteome efficient metabolism of individuals underlies metabolic interactions and the collective metabolism of microbial communities (Matthias)
- Factors that determine the degree of metabolic distribution in microbial ecosystems (Alyssa)
Cell lysis as a strategy for nutrient acquisition
- Contact-dependent antagonism and its role in nutrient acquisition in microbial communities (Astrid and Glen)
- Mathematical modeling of lysing dynamics and the resulting nutrient flow (Astrid and François Peaudecerf (Roman Stocker group))
- Bacterial adaptation and global effects of contact-dependent antagonism (Astrid)
- Effect of phage lysis in cross-feeding communities (Emanuele)
Method development
- Analysis software for live-cell imaging data (Franziska (ETH SIS), Glen, Astrid, Olga)
- Microfluidics platform combining measurements of single cell growth and ecophysiology (Glen, Astrid, Fabai Wu external page(Victoria Orphan group))
- Measurement techniques for studying community properties and ecosystem functions (CO2) in microbial communities
- Biosensor for cyanotoxins (Oliver Brandenberg (external pageEawag Uchem), Elisabeth Janssen (external pageEawag Uchem))
- Techniques for measuring protein post-translational modifications in microbiome samples (Noelle, Ludovic Gillet, Paola Picotti group)
- Anaerobic microfluidics (Alyson, Markus Arnoldini (Emma Slack group), external pageSusan Schlegel (Uppsala University))
- Microfluidic systems for exploring diverse microbial interactions (Stefano)